# 下载流程git clone https://github.com/nf-core/rnaseq.git 下载本地化镜像,并将设置镜像地址 # 在相同目录下,需在联网环境下 nf-core download --outdirsingularity/ --parallel-downloads 10 --container-system singularity rnaseq # 会跳出几个选项,选择默认的就行 # 设置镜像地址 export NXF_SINGULARI...
# 运行 nextflow sh nextflow-21.04.3-all run /nf-core-rnaseq-3.4/workflow \ # 格式就是nextflow run <下载好的nf-core-rnaseq文件夹下workflow文件夹的目录> --input samplesheet.csv \ # 就是上一步我们用python脚本生成的samplesheet.csv文件 --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa \...
tar-zxvf nf-core-rnaseq-3.4.tar.gz 此时我们可以通过nextflow运行这个安装包: 1 2 3 4 5 6 7 8 9 10 11 12 nextflow run nf-core-rnaseq-3.6/workflow/\# 格式就是nextflow run <下载好的nf-core-rnaseq文件夹下workflow文件夹的目录> --input samplesheet.csv \# 就是上一步我们用python脚本生成...
working with gene panels or single genes (e.g., NF1) in the nf-core/rnaseq pipeline #1472 openedDec 18, 2024byhuma1995 1 Unify SummarizedExperiment outputenhancement #1465 openedDec 10, 2024bygrst 2 ERROR Not able to pull image of ('biocontainers/bioconductor-tximeta:1.20.1--r43hdfd...
于是,NF-core应运而生。NF-core是利用Nextflow开发的生物流程共享中心,汇聚了众多优秀生物信息分析流程。目前,已经有81个涵盖多个生物信息领域的优秀流程,其中最经典的莫过于RNAseq。📊每个流程都配备了详细的介绍,包括简介、文档、结果展示以及选项参数。有些流程甚至还提供了视频讲解,是学习生物信息学的宝贵资源。
一般,一个离线流程包括源码,软件和配置文件。nf-core 提供了一个辅助工具 helper tool 帮助我们搭建。 运行nf-core list查看有哪些流程 离线下载nf-core/rnaseq nf-core download nf-core/rnaseq 加入--singularity,可以获取 Singularity container 什么是Singularity ?https://singularity.lbl.gov/ ...
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. - nf-core CI · Workflow runs · nf-core/rnaseq
# 加载 RNAseq pipeline nextflow run nf-core/rnaseq \ -profile docker \ --genome GRCh37 \ --reads "data/*_{R1,R2}.fastq.gz" # 安装nf-core pip install nf-core # 查看nf-core已有流程或者最新可用版本 nf-core list # 命令 nf-core list :列出可用pipeline ...
nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysisdoi:10.12688/wellcomeopenres.19453.1CLIPNextflowRNA-protein interactionsbioinformatic pipelinespeak callingreproducible researchCrosslinking and immunoprecipitation (CLIP) technologies have become a central component of the molecular ...
To address these shortcomings, we present nf-core/circrna, a workflow for the quan- tification, miRNA target prediction and differential expression analysis of circRNAs in RNA-Seq data developed using nextflow [28]. The pipeline has been developed under the specifications of the nf-core framework...